MolNFT v1 · #12275 · protein
Nitrite-soaked crystal structure of the soluble domain of ania from neisseria gonorrhoeae
1KBV · Major outer membrane protein pan 1: “Nitrite-soaked crystal structure of the soluble domain of ania from neisseria gonorrhoeae”. X-ray diffraction, 2 ligands (CU, NO2), 20 pockets (best druggability 0.83). MolNFT v1 #12275 on…
- PDB
- 1KBV
- Type
- protein
- Length
- 1,812 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major outer membrane protein pan 1
- UniProt
- Q02219
- Ligands
- CU, NO2
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Major outer membrane protein pan 1 | protein | 302 | 9% helix, 47% strand | Q02219 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C, D, E, F
- NO2 · Nitrite ion · ion · 6 copies · chains A, B, C, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.83 | 0.95 | 36 | empty |
| 2 | 258 | 0.82 | 0.94 | 37 | empty |
| 3 | 69 | 0.75 | 0.98 | 25 | empty |
| 4 | 63 | 0.71 | 0.97 | 19 | empty |
| 5 | 53 | 0.49 | 0.86 | 15 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1768 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1760 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 1744 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1743 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1733 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1KBV · Nitrite-soaked crystal structure of the soluble domain of ania from neisseria gonorrhoeae · the same entry in another collection · chain D against D, TM-score 1.00
- Q02219 · AlphaFold monomer V2.0 prediction for copper-containing nitrite reductase (Q02219) · a predicted model of the same protein · chain E against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q02219
- Elsewhere: RCSB PDB 1KBV · PDBe 1KBV · UniProt Q02219
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